Calcium in PDB 3qrb: Crystal Structure of E-Cadherin EC1-2 P5A P6A

The structure of Crystal Structure of E-Cadherin EC1-2 P5A P6A, PDB code: 3qrb was solved by X.Jin, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.70 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.185, 92.583, 79.465, 90.00, 92.26, 90.00
R / Rfree (%)	16.2 / 17.8

The binding sites of Calcium atom in the Crystal Structure of E-Cadherin EC1-2 P5A P6A (pdb code 3qrb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of E-Cadherin EC1-2 P5A P6A, PDB code: 3qrb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:13.5 occ:1.00 OE1 A:GLU69 2.2 19.6 1.0 OD1 A:ASP67 2.3 17.6 1.0 OD2 A:ASP103 2.3 19.2 1.0 OE1 A:GLU11 2.4 17.7 1.0 O A:HOH287 2.4 7.2 1.0 O A:HOH288 2.4 7.3 1.0 CG A:ASP103 3.1 18.9 1.0 OD1 A:ASP103 3.2 16.9 1.0 CG A:ASP67 3.3 17.7 1.0 CD A:GLU11 3.3 17.9 1.0 CD A:GLU69 3.5 18.6 1.0 OE2 A:GLU11 3.7 18.9 1.0 OD2 A:ASP67 4.0 17.5 1.0 CA A:CA302 4.0 13.6 1.0 N A:ARG68 4.1 15.2 1.0 CA A:ASP67 4.1 15.2 1.0 O A:HOH408 4.2 15.2 1.0 CB A:ASP67 4.2 16.2 1.0 N A:GLU69 4.2 16.9 1.0 CB A:GLU69 4.3 19.1 1.0 ND2 A:ASN104 4.3 15.6 1.0 CG A:GLU69 4.4 19.6 1.0 OE2 A:GLU69 4.4 19.9 1.0 C A:ASP67 4.4 15.9 1.0 OD1 A:ASN12 4.4 18.4 1.0 ND2 A:ASN12 4.4 20.1 1.0 O A:HOH215 4.6 18.8 1.0 O A:HOH239 4.6 19.8 1.0 CB A:ASP103 4.6 18.6 1.0 CG A:GLU11 4.6 17.6 1.0 O A:HOH602 4.6 20.9 1.0 CG A:ASN12 4.8 21.4 1.0 CA A:GLU69 4.8 17.9 1.0 CB A:GLU11 4.9 16.0 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:13.6 occ:1.00 OD1 A:ASP100 2.2 18.1 1.0 OE2 A:GLU11 2.3 18.9 1.0 OD1 A:ASP136 2.3 16.2 1.0 OD1 A:ASP103 2.3 16.9 1.0 OE2 A:GLU69 2.4 19.9 1.0 O A:GLN101 2.4 18.4 1.0 OE1 A:GLU69 2.7 19.6 1.0 CD A:GLU69 2.9 18.6 1.0 CG A:ASP100 3.3 18.1 1.0 CG A:ASP136 3.4 18.8 1.0 CD A:GLU11 3.4 17.9 1.0 CG A:ASP103 3.5 18.9 1.0 C A:GLN101 3.6 19.2 1.0 OE1 A:GLU11 3.8 17.7 1.0 N A:GLN101 3.8 19.0 1.0 OD2 A:ASP100 3.8 18.0 1.0 ND2 A:ASN104 3.9 15.6 1.0 CA A:CA301 4.0 13.5 1.0 CB A:ASP136 4.0 17.7 1.0 OD2 A:ASP103 4.0 19.2 1.0 N A:ASP103 4.1 19.1 1.0 CA A:ASP136 4.3 19.0 1.0 CG A:GLU69 4.3 19.6 1.0 OD2 A:ASP136 4.3 13.9 1.0 CA A:GLN101 4.3 20.0 1.0 NE A:ARG68 4.4 20.4 1.0 CB A:ASP100 4.5 18.6 1.0 CA A:ASP100 4.6 18.8 1.0 CB A:ASP103 4.6 18.6 1.0 N A:ASN102 4.7 19.3 1.0 C A:ASP100 4.7 19.4 1.0 CG A:GLU11 4.7 17.6 1.0 CA A:ASP103 4.8 19.1 1.0 CA A:ASN102 4.8 19.3 1.0 NH2 A:ARG68 4.8 21.7 1.0 CB A:ARG68 4.9 16.7 1.0 C A:ASN102 5.0 19.9 1.0 CB A:GLN101 5.0 20.5 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:16.4 occ:1.00 O A:ASN104 2.3 19.7 1.0 OD2 A:ASP136 2.3 13.9 1.0 O A:ASN143 2.3 19.4 1.0 OD1 A:ASN102 2.3 21.2 1.0 OD2 A:ASP195 2.3 20.6 1.0 OD2 A:ASP134 2.4 21.7 1.0 OD1 A:ASP134 2.6 20.2 1.0 CG A:ASP134 2.8 22.3 1.0 CG A:ASP195 3.4 21.4 1.0 CG A:ASP136 3.4 18.8 1.0 C A:ASN104 3.5 19.9 1.0 CG A:ASN102 3.5 19.6 1.0 C A:ASN143 3.5 18.8 1.0 CB A:ASP136 3.8 17.7 1.0 CB A:ASP195 3.8 20.3 1.0 ND2 A:ASN102 4.1 22.2 1.0 N A:ASN104 4.2 18.5 1.0 CA A:ASN104 4.3 19.3 1.0 CB A:ASP134 4.4 18.9 1.0 OD1 A:ASP195 4.4 21.4 1.0 CA A:ASN143 4.4 20.2 1.0 CB A:ASN104 4.5 18.7 1.0 CB A:ASN143 4.5 18.7 1.0 N A:ALA144 4.5 19.2 1.0 OD1 A:ASP136 4.5 16.2 1.0 N A:ARG105 4.6 21.3 1.0 CA A:ALA144 4.6 19.9 1.0 CD1 A:LEU201 4.7 20.9 1.0 CD A:PRO106 4.7 21.2 1.0 CB A:ASN102 4.7 19.9 1.0 CA A:ARG105 4.8 22.6 1.0 N A:ASP136 4.8 17.6 1.0 CA A:ASN102 4.8 19.3 1.0 C A:ARG105 4.9 22.0 1.0 N A:PRO106 4.9 21.9 1.0 CA A:ASP136 4.9 19.0 1.0 C A:ASN102 5.0 19.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:12.3 occ:1.00 OE1 B:GLU69 2.2 17.7 1.0 OD1 B:ASP67 2.3 17.1 1.0 OE1 B:GLU11 2.3 15.9 1.0 OD2 B:ASP103 2.3 17.2 1.0 O B:HOH533 2.4 6.6 1.0 O B:HOH537 2.4 8.2 1.0 CG B:ASP103 3.1 18.1 1.0 OD1 B:ASP103 3.2 17.3 1.0 CD B:GLU11 3.3 15.1 1.0 CG B:ASP67 3.3 16.6 1.0 CD B:GLU69 3.5 17.5 1.0 OE2 B:GLU11 3.6 16.4 1.0 CA B:CA302 3.9 12.9 1.0 OD2 B:ASP67 4.1 15.6 1.0 CA B:ASP67 4.1 14.7 1.0 N B:ARG68 4.2 14.5 1.0 CB B:ASP67 4.2 15.4 1.0 OD1 B:ASN104 4.2 19.9 1.0 O B:HOH253 4.3 10.2 1.0 N B:GLU69 4.3 14.7 1.0 OD1 B:ASN12 4.3 23.9 1.0 OE2 B:GLU69 4.3 17.3 1.0 CG B:GLU69 4.4 16.8 1.0 CB B:GLU69 4.4 16.3 1.0 C B:ASP67 4.4 15.3 1.0 O B:HOH383 4.4 14.6 1.0 CB B:ASP103 4.6 18.9 1.0 CG B:GLU11 4.6 16.9 1.0 ND2 B:ASN12 4.6 22.2 1.0 O B:HOH219 4.6 17.4 1.0 CB A:PRO46 4.7 18.9 1.0 CG B:ASN12 4.9 22.4 1.0 CB B:GLU11 4.9 16.4 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:12.9 occ:1.00 OD1 B:ASP100 2.2 17.1 1.0 OD1 B:ASP136 2.3 17.3 1.0 OE2 B:GLU11 2.3 16.4 1.0 OD1 B:ASP103 2.3 17.3 1.0 OE2 B:GLU69 2.4 17.3 1.0 O B:GLN101 2.5 17.5 1.0 OE1 B:GLU69 2.7 17.7 1.0 CD B:GLU69 2.9 17.5 1.0 CG B:ASP100 3.3 17.1 1.0 CG B:ASP136 3.4 17.2 1.0 CD B:GLU11 3.4 15.1 1.0 CG B:ASP103 3.4 18.1 1.0 C B:GLN101 3.6 18.1 1.0 OE1 B:GLU11 3.8 15.9 1.0 N B:GLN101 3.8 18.1 1.0 OD2 B:ASP100 3.9 16.9 1.0 CA B:CA301 3.9 12.3 1.0 OD1 B:ASN104 4.0 19.9 1.0 CB B:ASP136 4.0 16.1 1.0 OD2 B:ASP103 4.0 17.2 1.0 N B:ASP103 4.1 18.0 1.0 CA B:ASP136 4.2 16.2 1.0 CG B:GLU69 4.3 16.8 1.0 OD2 B:ASP136 4.3 16.6 1.0 CA B:GLN101 4.3 18.9 0.5 CA B:GLN101 4.3 18.8 0.5 NE B:ARG68 4.4 18.9 1.0 CB B:ASP100 4.5 17.2 1.0 CA B:ASP100 4.6 17.1 1.0 CB B:ASP103 4.6 18.9 1.0 N B:ASN102 4.7 18.6 1.0 C B:ASP100 4.7 18.6 1.0 CG B:GLU11 4.7 16.9 1.0 CA B:ASP103 4.8 18.9 1.0 CA B:ASN102 4.9 17.9 1.0 CB B:GLN101 4.9 19.4 0.5 NH2 B:ARG68 4.9 17.5 1.0 CB B:ARG68 4.9 14.9 1.0 C B:ASN102 5.0 18.9 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of E-Cadherin EC1-2 P5A P6A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of E-Cadherin EC1-2 P5A P6A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:15.8 occ:1.00 O B:ASN104 2.3 19.9 1.0 O B:ASN143 2.3 19.2 1.0 OD2 B:ASP195 2.3 19.4 1.0 OD1 B:ASN102 2.3 19.4 1.0 OD2 B:ASP136 2.4 16.6 1.0 OD2 B:ASP134 2.4 21.0 1.0 OD1 B:ASP134 2.6 19.1 1.0 CG B:ASP134 2.8 20.8 1.0 CG B:ASP195 3.3 21.6 1.0 CG B:ASP136 3.4 17.2 1.0 C B:ASN104 3.5 20.2 1.0 CG B:ASN102 3.5 19.2 1.0 C B:ASN143 3.5 18.2 1.0 CB B:ASP195 3.8 19.7 1.0 CB B:ASP136 3.8 16.1 1.0 ND2 B:ASN102 4.1 17.9 1.0 N B:ASN104 4.2 18.2 1.0 CA B:ASN104 4.3 19.5 1.0 OD1 B:ASP195 4.3 21.3 1.0 CB B:ASP134 4.4 19.0 1.0 CA B:ASN143 4.4 19.4 1.0 CB B:ASN143 4.4 18.4 1.0 N B:ALA144 4.5 18.9 1.0 CB B:ASN104 4.5 18.4 1.0 N B:ARG105 4.5 22.0 1.0 OD1 B:ASP136 4.6 17.3 1.0 CA B:ALA144 4.6 19.2 1.0 CD1 B:LEU201 4.7 22.3 1.0 CA B:ARG105 4.7 23.2 0.5 CB B:ASN102 4.7 18.8 1.0 CA B:ARG105 4.8 22.8 0.5 N B:ASP136 4.8 15.4 1.0 CD B:PRO106 4.8 22.5 1.0 C B:ARG105 4.8 23.0 1.0 CA B:ASN102 4.8 17.9 1.0 N B:PRO106 4.9 22.6 1.0 CA B:ASP136 5.0 16.2 1.0 C B:ASN102 5.0 18.9 1.0

J.Vendome, S.Posy, X.Jin, F.Bahna, G.Ahlsen, L.Shapiro, B.Honig. Molecular Design Principles Underlying Beta-Strand Swapping in the Adhesive Dimerization of Cadherins. Nat.Struct.Mol.Biol. V. 18 693 2011.
ISSN: ISSN 1545-9993
PubMed: 21572446
DOI: 10.1038/NSMB.2051